We just lately posted the following paper which offers an extension of the SHAPEIT model that enables to get in touch with genotype from minimal protection sequencing knowledge when a chip-derived haplotype scaffold is readily available for exactly the same list of samples:
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* Small: When output window coordinates are not consistent with input window coordinates, These are automatically set
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The initial column provides the sample ID corresponding to the BAM file. This sample ID must match one of the sample ID in the VCF to ensure my sources that extractPIRs to effectively map sequencing reads to samples.
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